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Detailed information for vg0715058787:

Variant ID: vg0715058787 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15058787
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CATGATCTGATGGACCACCACCTAATCACAAACAAAACCTTAGCAAACATATTCAAACATGCGTATAAAACTATGAAAAAGGTGAACCTACTGCCCCATC[C/T]
CATCAAAACTCAATAACAAGGAACGCCGCTTGGACTATACACAGGACTGCTGCTTCAAACCTTTATATCTTGAAATATGAAAAGGCTATGACTGAAAATG

Reverse complement sequence

CATTTTCAGTCATAGCCTTTTCATATTTCAAGATATAAAGGTTTGAAGCAGCAGTCCTGTGTATAGTCCAAGCGGCGTTCCTTGTTATTGAGTTTTGATG[G/A]
GATGGGGCAGTAGGTTCACCTTTTTCATAGTTTTATACGCATGTTTGAATATGTTTGCTAAGGTTTTGTTTGTGATTAGGTGGTGGTCCATCAGATCATG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.20%	2.90%	6.96%	2.98%	NA
All Indica	2759	84.20%	4.20%	9.97%	1.70%	NA
All Japonica	1512	90.50%	0.50%	2.91%	6.08%	NA
Aus	269	93.70%	4.10%	2.23%	0.00%	NA
Indica I	595	79.70%	3.00%	15.63%	1.68%	NA
Indica II	465	88.20%	0.60%	9.03%	2.15%	NA
Indica III	913	80.20%	8.20%	9.42%	2.19%	NA
Indica Intermediate	786	89.80%	2.40%	6.87%	0.89%	NA
Temperate Japonica	767	81.70%	1.00%	5.35%	11.86%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	93.30%	1.10%	4.44%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715058787	C -> DEL	N	N	silent_mutation	Average:11.921; most accessible tissue: Callus, score: 38.789	N	N	N	N
vg0715058787	C -> T	LOC_Os07g26180.1	downstream_gene_variant ; 1705.0bp to feature; MODIFIER	silent_mutation	Average:11.921; most accessible tissue: Callus, score: 38.789	N	N	N	N
vg0715058787	C -> T	LOC_Os07g26190.1	downstream_gene_variant ; 1087.0bp to feature; MODIFIER	silent_mutation	Average:11.921; most accessible tissue: Callus, score: 38.789	N	N	N	N
vg0715058787	C -> T	LOC_Os07g26200.1	downstream_gene_variant ; 4539.0bp to feature; MODIFIER	silent_mutation	Average:11.921; most accessible tissue: Callus, score: 38.789	N	N	N	N
vg0715058787	C -> T	LOC_Os07g26180-LOC_Os07g26190	intergenic_region ; MODIFIER	silent_mutation	Average:11.921; most accessible tissue: Callus, score: 38.789	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715058787	2.10E-06	NA	mr1620	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251